It is increasing clear that biofuels can be a viable source of renewable energy in contrast to the finite nature, geopolitical instability, and deleterious global effects of fossil fuel energy. Collectively, biofuels include any energy-enriched chemicals generated directly through the biological processes or derived from the chemical conversion from biomass of prior living organisms. Predominantly, biofuels are produced from photosynthetic organisms such as photosynthetic bacteria, micro- and macro-algae and vascular land plants. The primary products of biofuel may be in a gas, liquid, or solid form. These products can be further converted by biochemical, physical, and thermochemical methods. Biofuels can be classified into two categories: primary and secondary biofuels. The primary biofuels are directly produced from burning woody or cellulosic plant material and dry animal waste. The secondary biofuels can be classified into three generations that are each indirectly generated from plant and animal material. The first generation of biofuels is ethanol derived from food crops rich in starch or biodiesel taken from waste animal fats such as cooking grease. The second generation is bioethanol derived from non-food cellulosic biomass and biodiesel taken from oil-rich plant seed such as soybean or jatropha. The third generation is the biofuels generated from cyanobacterial, microalgae and other microbes, which is the most promising approach to meet the global energy demands. In this review, we present the recent progresses including challenges and opportunities in microbial biofuels production as well as the potential applications of microalgae as a platform of biomass production. Future research endeavors in biofuel production should be placed on the search of novel biofuel production species, optimization and improvement of culture conditions, genetic engineering of biofuel-producing species, complete understanding of the biofuel production mechanisms, and effective techniques for mass cultivation of microorganisms. (C) 2016 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.